9-97819742-A-G

Variant names:

• chr9-97819742-A-G
• rs6478413
• ENST00000649253.2:n.166-9703T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_147055.1(PTCSC2):​n.166-9703T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,956 control chromosomes in the GnomAD database, including 33,845 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.66 (33845 hom., cov: 30)
• Consequence: PTCSC2 NR_147055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 4 publications found

Genes affected

PTCSC2 (HGNC:44086): (papillary thyroid carcinoma susceptibility candidate 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_147055.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	NR_147055.1		n.166-9703T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000649253.2		n.166-9703T>C		intron	N/A
	PTCSC2	ENST00000649461.1		n.166-9703T>C		intron	N/A
	PTCSC2	ENST00000649526.1		n.166-9703T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100016 AN: 151838 Hom.: 33809 Cov.: 30

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.664

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.659 AC: 100097 AN: 151956 Hom.: 33845 Cov.: 30 AF XY: 0.661 AC XY: 49117 AN XY: 74260

African (AFR) AF: 0.779 AC: 32269 AN: 41436

American (AMR) AF: 0.648 AC: 9898 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2049 AN: 3470

East Asian (EAS) AF: 0.986 AC: 5110 AN: 5184

South Asian (SAS) AF: 0.679 AC: 3264 AN: 4810

European-Finnish (FIN) AF: 0.578 AC: 6087 AN: 10536

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39496 AN: 67944

Other (OTH) AF: 0.663 AC: 1394 AN: 2102

Alfa AF: 0.637 Hom.: 6504

Bravo AF: 0.672

Asia WGS AF: 0.807 AC: 2809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.1
DANN	Benign	0.86
PhyloP100		0.16

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6478413; hg19: chr9-100582024;